REFMAC (CCP4: Supported Program)
User's manual for the program refmac_5.0.36
KEYWORDED INPUT
Anything input on a line after "!" or "#" is ignored and lines can be continued by using a minus (-) sign. The program only checks the first 4 characters of each keyword. The order of the cards is not important except that an END card must be last. Some keywords have various subsidiary keywords. The available keywords in alphabetical order are:
ANGLe, BFACtor/TEMPerature, BINS/RANGE, BLIMit, CELL_parameters, CHIRal_volumes, DAMPing_factor, DISTance, DNAME, END/GO, FREE, HOLD, LABIn, LABOut, MAKE_restraints, MODE, MONItor, NCYCle, NCSR/NONX, NOHARVEST, PHASe, PLANe, PNAME, PRIVATE, RBONd, REFInement, RIGId_body, RSIZE, SCALe, SCPArt, SHANnon_factor, SIGMaA, SOLVent, SPHEricity, SYMM, TLSC, TORSION, USECWD, VDWR/VAND, WEIG,
- Principal keywords controlling Xray refinement:
- LABI - Input MTZ labels
- NCYC - Number of the refinement cycles
- REFI - Refinement parameters
- SCAL - Scale parameters
- SIGM - Parameters of the likelihood (sigmaA)
- SOLV - Parameters of the solvent
- WEIG - Weighting X-ray vs geometry
- All keywords for Xray refinement:
- BINS/RANGE - Number of the resolution bins
- BLIM - Limits of allowed B value range
- CELL - Cell parameters
- DAMP - Factors to scale down shifts at every cycle
- END/GO - End of keywords; must be last
- FREE - Flag of the reflections excluded from the refinement
- LABO - Output MTZ labels. Useful for map calculation
- MODE - Refinement mode
- MONI - Level of monitoring statistics during refinement
- PHAS - Parameters for the phased refinement
- RIGI - Parameters of the rigid body refinement
- SCPA - For scaling of the external partial structure factors
- SHAN - Shannon factor to control grid spacings
- SYMM - Symmetry
- TLSC - Number of TLS cycles
- Keywords controlling (geometric) restraints (function very similar to that in PROLSQ):
- ANGL - Restraints on bond angles
- BFAC/TEMP - Restraints on B values
- CHIR - Restraints on chiral volumes
- DIST - Restraints on bond distances
- HOLD - Restraints against excessive shifts
- MAKE - Controls making restraints and checking coordinates against dictionary
- NCSR/NONX - Restraints on non-crystallographic symmetry
- PLAN - Restraints on planarity
- RBON - Rigid bond restraints on the anisotropic B values of bonded atoms
- SPHE - Sphericity restraints on the anisotropic B values
- TORS - Restraints on the torsion angles
- VDWR/VAND - Restraints on VDW repulsions
- Optional keywords controlling the data harvesting functionality:
- DNAME - Dataset name
- NOHARVEST - Harvesting files are not necessary
- PNAME - Project name
- PRIVATE - Controls modes of the files created for harvesting
- RSIZE - Number of characters in one column
- USECWD - Controls directory where harvesting files are